##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetSAM_1.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/NetSAM.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetSAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NetSAM’ version ‘1.39.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NetSAM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘NetSAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapToSymbol
> ### Title: Map other ids to gene symbols
> ### Aliases: mapToSymbol
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	
> 	###transform ids from a gene list to gene symbols###
> 	geneListDir <- system.file("extdata","exampleGeneList.txt",package="NetSAM")
> 	geneList <- read.table(geneListDir,header=FALSE,sep="\t",stringsAsFactors=FALSE)
> 	geneList <- as.vector(as.matrix(geneList))
> 	geneList_symbol <- mapToSymbol(inputData=geneList, organism="hsapiens", inputType="genelist",idType="affy_hg_u133_plus_2")
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
> 	
> 	###transform ids in the input network to gene symbols###
> 	inputNetwork <- system.file("extdata","exampleNetwork_nonsymbol.net",package="NetSAM")
> 	network_symbol <- mapToSymbol(inputData=inputNetwork,organism="hsapiens",inputType="network",idType="entrezgene_id",edgeType="unweighted")
Transforming the ids in the input network to gene symbols...
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Error in .GeneToSymbol(netNode, organism, idType, verbose) : 
  The function can not connect to Biomart. Please try again!
Calls: mapToSymbol -> .NetToSymbol -> .GeneToSymbol
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetSAM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘NetSAM’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NetSAM)

R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("NetSAM")

Attaching package: 'igraph'

The following object is masked from 'package:seriation':

    permute

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust



Attaching package: 'WGCNA'

The following object is masked from 'package:stats':

    cor

******************************************

*            Welcome to NetSAM !         *

******************************************


Allowing multi-threading with up to 3 threads.

Identifying the hierarchical modules of the network...
Starting to analysis connected component 1!
Evaluating networks in Level 1 ...
Network modularity: 0.5512183

Evaluating networks in Level 2 ...
Modularity of network 1: 0.2083333

Modularity of network 2: 0.2915519

Modularity of network 3: 0.377551

Modularity of network 4: 0.4114896

Modularity of network 5: 0.3669114

Modularity of network 6: 0.4228597

Modularity of network 7: 0.25

Modularity of network 8: 0.1985731

Modularity of network 9: 0.21875

Modularity of network 10: 0.07986111

Modularity of network 11: 0

Evaluating networks in Level 3 ...
Modularity of network 1: 0

Modularity of network 2: 0.2040816

Modularity of network 3: 0.1417769

Modularity of network 4: 0.3047337